I seemed to have had similar issues but now have my aimtrak running well. Here are some things I did to improve the performance:
1. Moved the lightbar closer to the monitor. I drilled some holes in the monitor bezel and mounted the lightbar behind the bezel, just above the monitor. This improved the response dramatically.
2. Double check your mame.ini settings. The aimtrak has very specific settings that need to be followed or it won't work correctly. I missed this the first time around.
3. I am assuming that you are using the gun to set the x and y axis? If so, you may find it easier to manually edit the default.cfg. I found this to be easier than using trying to ensure I was moving the gun on only the x or y axis during setup.
4. Calibrate the guns at the same resolution of the game you are playing. Also, there are some game specific settings that may also help you by hitting F2 from within the game.
Played Area51 last night without issues and I will say that the guns add a nice touch to my cab.
Also, don't hesitate to reach out to Andy at Ultimarc. He is very responsive and truly stands behind his products.